Nextstrain-augur

Features

* schemas: Add "$id" key to Auspice config schemas so we have a way of referring to these. [806][] (tsibley)

Bug Fixes

* filter: Fix groupby with incomplete dates. [808][] (victorlin)

[806]: https://github.com/nextstrain/augur/pull/806
[808]: https://github.com/nextstrain/augur/pull/808

Bug Fixes

* dependencies: Replace deprecated mutable sequence interface for BioPython. [788][] (Carlosbogo)
* dependencies: Fix backward compatibility with BioPython. [801][] (huddlej)
* data: Add latitude and longitude details for "Reunion". [791][] (corneliusroemer)
* filter: Use pandas functions to determine subsample groups. [794][] and [797][] (victorlin)
* filter: Add clarity to help message and output of probabilistic sampling. [792][] (victorlin)

[788]: https://github.com/nextstrain/augur/pull/788
[791]: https://github.com/nextstrain/augur/pull/791
[792]: https://github.com/nextstrain/augur/pull/792
[794]: https://github.com/nextstrain/augur/pull/794
[797]: https://github.com/nextstrain/augur/pull/797
[801]: https://github.com/nextstrain/augur/pull/801

Bug Fixes

* tree: Handle compressed alignment when excluding sites. [786][] (huddlej)
* docs: Fix typos ([ce0834c][]) and clarify exclude sites inputs ([5ad1574][]). (corneliusroemer)

[786]: https://github.com/nextstrain/augur/pull/786
[ce0834c]: https://github.com/nextstrain/augur/commit/ce0834c476abc9ee99785fa930608218b7d78990
[5ad1574]: https://github.com/nextstrain/augur/commit/5ad157485015623883c6b637d247459f906b63cb

Bug Fixes

* dependencies: Support latest versions of BioPython. [777][] (huddlej)
* tree: Allow users to specify arbitrary IQ-TREE models. [776][] (huddlej)

[776]: https://github.com/nextstrain/augur/pull/776
[777]: https://github.com/nextstrain/augur/pull/777

Bug Fixes

* docs: Fix broken link to latitude/longitude documentation. [766][] (victorlin)
* filter: Fix reproducibility of subsampling by using the user-defined random seed in all random function calls and by ordering strain sets as lists prior to adding strains to group-by priority queues. [772][] (huddlej)

[766]: https://github.com/nextstrain/augur/pull/766
[772]: https://github.com/nextstrain/augur/pull/772

Major Changes

* filter: Skip metadata records with ambiguous month information in the `date` column when grouping by month instead of randomly generating month values for those records. This change alters the behavior of the `filter` command for metadata with ambiguous month values. For these data, consider using `--group-by year` instead of `--group-by year month`. [761][] (huddlej)

Features

* filter: When grouping by year or month, report the number of strains skipped due to ambiguous year and month both in the summary report at the end of filtering and in the `--output-log` contents [761][] (huddlej)

[761]: https://github.com/nextstrain/augur/pull/761